Quality Control And Differentiall Gene Expression Results

This Is A Report Of Quality Control And Differentail Gene Expression Analysis.

Differential Gene Expression Approach Used: DESeq2

Cutoffs To Establish Differentially Regulated Genes: |Log2FC| > 0.5 & padj < 0.1

PCA Plots

2D PCA on DESeq2’s Normalized Counts
Total Explained Variance = 65.512%
3D PCA on DESeq2’s Normalized Counts
Total Explained Variance = 77.624%
2D PCA on DESeq2’s Normalized Counts
Total Explained Variance = 93.72%
3D PCA on DESeq2’s Normalized Counts
Total Explained Variance = 97.447%

Dendrograms representing sample clustering

Dendrogram on DESeq2’s Normalized Counts

Dendrogram on DESeq2 normalized counts with only DEGs

Correlation between samples performed on Euclidean distance with the use of DE genes

Volcano Plots

Differentially Regulated Genes - Visualized Interactively

Top 30 most significant GO and KEGG Terms respectively - Visualized Interactively

Top 30 most significant GO Terms

ID Description setSize enrichmentScore NES pvalue p.adjust qvalues rank
GO:0001819 GO:0001819 positive regulation of cytokine production 396 -0.5437645 -1.891616 0 0 0 4170
GO:0002377 GO:0002377 immunoglobulin production 171 -0.7441810 -2.404630 0 0 0 2023
GO:0002429 GO:0002429 immune response-activating cell surface receptor signaling pathway 429 -0.6409283 -2.240673 0 0 0 2354
GO:0002431 GO:0002431 Fc receptor mediated stimulatory signaling pathway 131 -0.7457044 -2.347834 0 0 0 2061
GO:0002433 GO:0002433 immune response-regulating cell surface receptor signaling pathway involved in phagocytosis 125 -0.7543619 -2.357009 0 0 0 2061
GO:0002440 GO:0002440 production of molecular mediator of immune response 252 -0.6801668 -2.290847 0 0 0 3216
GO:0002449 GO:0002449 lymphocyte mediated immunity 315 -0.6405384 -2.197916 0 0 0 2112
GO:0002455 GO:0002455 humoral immune response mediated by circulating immunoglobulin 127 -0.7486526 -2.340476 0 0 0 1968
GO:0002460 GO:0002460 adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains 325 -0.6526521 -2.248977 0 0 0 2666
GO:0002696 GO:0002696 positive regulation of leukocyte activation 355 -0.6014359 -2.081057 0 0 0 3811
GO:0002697 GO:0002697 regulation of immune effector process 422 -0.5415236 -1.888603 0 0 0 3812
GO:0002757 GO:0002757 immune response-activating signal transduction 429 -0.6409283 -2.240673 0 0 0 2354
GO:0002764 GO:0002764 immune response-regulating signaling pathway 463 -0.6334047 -2.223575 0 0 0 2354
GO:0002768 GO:0002768 immune response-regulating cell surface receptor signaling pathway 460 -0.6346949 -2.226791 0 0 0 2354
GO:0002920 GO:0002920 regulation of humoral immune response 118 -0.6813702 -2.112765 0 0 0 1968
GO:0003823 GO:0003823 antigen binding 130 -0.7394056 -2.327325 0 0 0 2039
GO:0005930 GO:0005930 axoneme 121 0.6380063 2.285192 0 0 0 3801
GO:0006898 GO:0006898 receptor-mediated endocytosis 301 -0.6331288 -2.167733 0 0 0 1970
GO:0006909 GO:0006909 phagocytosis 338 -0.6558300 -2.260057 0 0 0 2496
GO:0006911 GO:0006911 phagocytosis, engulfment 104 -0.7692759 -2.345129 0 0 0 1933
GO:0006956 GO:0006956 complement activation 142 -0.7245575 -2.300670 0 0 0 1937
GO:0006958 GO:0006958 complement activation, classical pathway 112 -0.7625066 -2.346198 0 0 0 1937
GO:0006959 GO:0006959 humoral immune response 287 -0.6101941 -2.082021 0 0 0 2343
GO:0007018 GO:0007018 microtubule-based movement 343 0.4780596 1.921212 0 0 0 4605
GO:0008037 GO:0008037 cell recognition 199 -0.6120655 -2.007851 0 0 0 2150
GO:0009897 GO:0009897 external side of plasma membrane 358 -0.6154264 -2.130194 0 0 0 3703
GO:0010324 GO:0010324 membrane invagination 120 -0.7509297 -2.334092 0 0 0 1933
GO:0016064 GO:0016064 immunoglobulin mediated immune response 191 -0.7176371 -2.354378 0 0 0 1968
GO:0019724 GO:0019724 B cell mediated immunity 194 -0.7159163 -2.344725 0 0 0 1968
GO:0019814 GO:0019814 immunoglobulin complex 121 -0.8466625 -2.641557 0 0 0 1933

Top 30 most significant KEGG Pathways

Description setSize enrichmentScore NES pvalue p.adjust qvalues rank leading_edge
hsa04060 Cytokine-cytokine receptor interaction 237 -0.5728888 -1.934321 0.0000000 0.0000004 0.0000004 3661 tags=46%, list=17%, signal=38%
hsa04380 Osteoclast differentiation 116 -0.6187328 -1.936975 0.0000002 0.0000400 0.0000362 4483 tags=42%, list=21%, signal=34%
hsa04061 Viral protein interaction with cytokine and cytokine receptor 84 -0.6492343 -1.954523 0.0000013 0.0001354 0.0001227 3357 tags=54%, list=15%, signal=46%
hsa05143 African trypanosomiasis 34 -0.7314140 -1.906165 0.0000957 0.0077550 0.0070294 2996 tags=50%, list=14%, signal=43%
hsa05144 Malaria 45 -0.6691906 -1.829394 0.0002593 0.0168045 0.0152321 2996 tags=44%, list=14%, signal=38%
hsa04062 Chemokine signaling pathway 172 -0.4892680 -1.602290 0.0003909 0.0211089 0.0191338 3082 tags=27%, list=14%, signal=23%
hsa04145 Phagosome 133 -0.5084017 -1.618602 0.0005194 0.0240410 0.0217916 2991 tags=25%, list=14%, signal=22%
hsa04625 C-type lectin receptor signaling pathway 96 -0.5496769 -1.672728 0.0006067 0.0245732 0.0222739 4225 tags=32%, list=19%, signal=26%
hsa05152 Tuberculosis 155 -0.4868189 -1.573718 0.0007506 0.0270228 0.0244944 4942 tags=34%, list=23%, signal=26%
hsa04080 Neuroactive ligand-receptor interaction 272 -0.4341123 -1.479482 0.0010016 0.0324516 0.0294152 2804 tags=31%, list=13%, signal=27%
hsa04662 B cell receptor signaling pathway 73 -0.5636494 -1.651019 0.0016835 0.0495854 0.0449459 3655 tags=27%, list=17%, signal=23%
hsa05205 Proteoglycans in cancer 199 -0.4471671 -1.484681 0.0022090 0.0596421 0.0540616 3732 tags=24%, list=17%, signal=20%
hsa05340 Primary immunodeficiency 33 -0.6626406 -1.725614 0.0029925 0.0662150 0.0600195 3094 tags=61%, list=14%, signal=52%
hsa05414 Dilated cardiomyopathy 92 -0.5247765 -1.596397 0.0030361 0.0662150 0.0600195 3523 tags=34%, list=16%, signal=28%
hsa04659 Th17 cell differentiation 101 -0.5054507 -1.549432 0.0030655 0.0662150 0.0600195 4024 tags=36%, list=18%, signal=29%
hsa04666 Fc gamma R-mediated phagocytosis 92 -0.5170513 -1.572896 0.0042907 0.0868858 0.0787562 4308 tags=25%, list=20%, signal=20%
hsa04730 Long-term depression 57 -0.5749751 -1.630755 0.0051956 0.0948724 0.0859955 4605 tags=39%, list=21%, signal=31%
hsa03010 Ribosome 126 0.4154256 1.481365 0.0052707 0.0948724 0.0859955 8549 tags=71%, list=39%, signal=44%
hsa04360 Axon guidance 174 -0.4432090 -1.454350 0.0060811 0.1029028 0.0932745 5744 tags=39%, list=26%, signal=29%
hsa04514 Cell adhesion molecules 143 -0.4644479 -1.496108 0.0063520 0.1029028 0.0932745 3446 tags=37%, list=16%, signal=31%
hsa05410 Hypertrophic cardiomyopathy 88 -0.5096512 -1.548758 0.0067624 0.1043339 0.0945717 3523 tags=34%, list=16%, signal=29%
hsa04613 Neutrophil extracellular trap formation 135 -0.4577221 -1.461744 0.0084436 0.1175908 0.1065881 2231 tags=17%, list=10%, signal=15%
hsa04974 Protein digestion and absorption 92 -0.5007167 -1.523205 0.0086237 0.1175908 0.1065881 4470 tags=47%, list=20%, signal=37%
hsa05321 Inflammatory bowel disease 62 -0.5469064 -1.567591 0.0092254 0.1175908 0.1065881 3827 tags=42%, list=18%, signal=35%
hsa04658 Th1 and Th2 cell differentiation 85 -0.4985516 -1.503809 0.0092539 0.1175908 0.1065881 4024 tags=38%, list=18%, signal=31%
hsa05150 Staphylococcus aureus infection 71 -0.5267601 -1.538898 0.0094363 0.1175908 0.1065881 2494 tags=37%, list=11%, signal=33%
hsa05140 Leishmaniasis 72 -0.5219597 -1.526111 0.0111411 0.1336929 0.1211836 2996 tags=31%, list=14%, signal=26%
hsa04650 Natural killer cell mediated cytotoxicity 97 -0.4750737 -1.445189 0.0155714 0.1801833 0.1633240 3149 tags=39%, list=14%, signal=34%
hsa05226 Gastric cancer 140 -0.4361604 -1.402568 0.0180397 0.2015475 0.1826893 4955 tags=30%, list=23%, signal=23%
hsa04270 Vascular smooth muscle contraction 123 -0.4422695 -1.398689 0.0189871 0.2050609 0.1858739 5715 tags=45%, list=26%, signal=33%

Top 30 most significant WIKI Pathways

Description setSize enrichmentScore NES pvalue p.adjust qvalues rank leading_edge
WP4803 Ciliopathies 174 0.5151399 1.931770 0.0000000 0.0000236 0.0000216 5577 tags=63%, list=26%, signal=47%
WP4536 Genes related to primary cilium development (based on CRISPR) 100 0.5335058 1.879537 0.0000186 0.0051748 0.0047332 7296 tags=74%, list=33%, signal=49%
WP5055 Burn wound healing 95 -0.5742072 -1.752016 0.0000546 0.0101434 0.0092779 4582 tags=51%, list=21%, signal=40%
WP455 GPCRs, class A rhodopsin-like 177 -0.5037587 -1.646494 0.0001087 0.0151380 0.0138464 2612 tags=36%, list=12%, signal=32%
WP3945 TYROBP causal network in microglia 59 -0.6313851 -1.807226 0.0001540 0.0171534 0.0156898 5367 tags=56%, list=25%, signal=42%
WP3937 Microglia pathogen phagocytosis pathway 36 -0.7042751 -1.855815 0.0002573 0.0219657 0.0200915 1994 tags=36%, list=9%, signal=33%
WP5095 Overview of proinflammatory and profibrotic mediators 86 -0.5681335 -1.707930 0.0003127 0.0219657 0.0200915 2996 tags=48%, list=14%, signal=41%
WP3929 Chemokine signaling pathway 153 -0.5020828 -1.618328 0.0003155 0.0219657 0.0200915 3321 tags=27%, list=15%, signal=23%
WP2873 Aryl hydrocarbon receptor pathway 40 -0.6614129 -1.780444 0.0005981 0.0370133 0.0338552 3615 tags=40%, list=17%, signal=33%
WP129 Matrix metalloproteinases 28 -0.7198671 -1.804588 0.0007881 0.0430571 0.0393832 3091 tags=50%, list=14%, signal=43%
WP477 Cytoplasmic ribosomal proteins 86 0.4845100 1.655067 0.0008503 0.0430571 0.0393832 7695 tags=78%, list=35%, signal=51%

Top 30 most significant Reactome Pathways

Description setSize enrichmentScore NES pvalue p.adjust qvalues rank leading_edge
R-HSA-198933 Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell 115 -0.6885328 -2.152382 0.0000000 0.0000001 0.0000001 3226 tags=49%, list=15%, signal=42%
R-HSA-6798695 Neutrophil degranulation 451 -0.4907592 -1.715590 0.0000000 0.0000052 0.0000050 3124 tags=20%, list=14%, signal=17%
R-HSA-500792 GPCR ligand binding 366 -0.4903742 -1.698256 0.0000001 0.0000543 0.0000528 3084 tags=36%, list=14%, signal=31%
R-HSA-373076 Class A/1 (Rhodopsin-like receptors) 263 -0.5124662 -1.724093 0.0000003 0.0001125 0.0001094 3084 tags=38%, list=14%, signal=33%
R-HSA-375276 Peptide ligand-binding receptors 155 -0.5316774 -1.724738 0.0000146 0.0043237 0.0042036 2529 tags=42%, list=12%, signal=37%
R-HSA-2173782 Binding and Uptake of Ligands by Scavenger Receptors 41 -0.7104568 -1.911377 0.0000566 0.0139539 0.0135660 3312 tags=56%, list=15%, signal=48%
R-HSA-380108 Chemokine receptors bind chemokines 49 -0.6860329 -1.893186 0.0000771 0.0162979 0.0158450 3321 tags=59%, list=15%, signal=50%
R-HSA-1474228 Degradation of the extracellular matrix 133 -0.5280464 -1.687558 0.0002110 0.0389995 0.0379156 4867 tags=46%, list=22%, signal=36%
R-HSA-1442490 Collagen degradation 61 -0.6298463 -1.796123 0.0002487 0.0408761 0.0397400 5375 tags=62%, list=25%, signal=47%
R-HSA-1474244 Extracellular matrix organization 288 -0.4387761 -1.490951 0.0004343 0.0642335 0.0624482 5100 tags=47%, list=23%, signal=36%
R-HSA-5660526 Response to metal ions 10 0.8466431 1.829864 0.0008172 0.1098793 0.1068255 1688 tags=70%, list=8%, signal=65%
R-HSA-5654706 FRS-mediated FGFR3 signaling 18 -0.7664477 -1.753410 0.0014480 0.1319155 0.1282492 2671 tags=39%, list=12%, signal=34%
R-HSA-156827 L13a-mediated translational silencing of Ceruloplasmin expression 105 0.4513058 1.595706 0.0015776 0.1319155 0.1282492 8285 tags=76%, list=38%, signal=47%
R-HSA-72706 GTP hydrolysis and joining of the 60S ribosomal subunit 106 0.4479969 1.584252 0.0015846 0.1319155 0.1282492 8285 tags=75%, list=38%, signal=47%
R-HSA-8948216 Collagen chain trimerization 43 -0.6351886 -1.718056 0.0016029 0.1319155 0.1282492 4366 tags=58%, list=20%, signal=47%
R-HSA-156902 Peptide chain elongation 85 0.4726191 1.638073 0.0017129 0.1319155 0.1282492 7725 tags=78%, list=35%, signal=50%
R-HSA-1650814 Collagen biosynthesis and modifying enzymes 66 -0.5775922 -1.675247 0.0017580 0.1319155 0.1282492 4366 tags=50%, list=20%, signal=40%
R-HSA-192823 Viral mRNA Translation 85 0.4704329 1.630496 0.0018434 0.1319155 0.1282492 7725 tags=76%, list=35%, signal=50%
R-HSA-202733 Cell surface interactions at the vascular wall 122 -0.4933475 -1.552663 0.0019174 0.1319155 0.1282492 3761 tags=28%, list=17%, signal=23%
R-HSA-72613 Eukaryotic Translation Initiation 113 0.4454122 1.593479 0.0019211 0.1319155 0.1282492 8285 tags=73%, list=38%, signal=45%
R-HSA-72737 Cap-dependent Translation Initiation 113 0.4454122 1.593479 0.0019211 0.1319155 0.1282492 8285 tags=73%, list=38%, signal=45%
R-HSA-2408557 Selenocysteine synthesis 89 0.4680878 1.627473 0.0019622 0.1319155 0.1282492 7725 tags=75%, list=35%, signal=49%
R-HSA-9633012 Response of EIF2AK4 (GCN2) to amino acid deficiency 97 0.4579798 1.605021 0.0020549 0.1321399 0.1284674 7725 tags=73%, list=35%, signal=47%
R-HSA-2408522 Selenoamino acid metabolism 111 0.4378874 1.560744 0.0022732 0.1400878 0.1361944 7725 tags=67%, list=35%, signal=43%
R-HSA-72764 Eukaryotic Translation Termination 89 0.4579869 1.592354 0.0027867 0.1446001 0.1405813 7725 tags=74%, list=35%, signal=48%
R-HSA-3000480 Scavenging by Class A Receptors 19 -0.7412537 -1.707823 0.0028152 0.1446001 0.1405813 3045 tags=58%, list=14%, signal=50%
R-HSA-927802 Nonsense-Mediated Decay (NMD) 106 0.4340876 1.535065 0.0028167 0.1446001 0.1405813 8242 tags=69%, list=38%, signal=43%
R-HSA-975957 Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) 106 0.4340876 1.535065 0.0028167 0.1446001 0.1405813 8242 tags=69%, list=38%, signal=43%
R-HSA-2172127 DAP12 interactions 34 -0.6568122 -1.712451 0.0028800 0.1446001 0.1405813 2659 tags=32%, list=12%, signal=28%
R-HSA-72689 Formation of a pool of free 40S subunits 97 0.4517202 1.583084 0.0029331 0.1446001 0.1405813 8285 tags=78%, list=38%, signal=49%

Top 30 most significant Disease Ontology - DO - Disease Ontology

Description setSize enrichmentScore NES pvalue p.adjust qvalues rank leading_edge
DOID:37 skin disease 304 -0.5441697 -1.857470 0.0000000 0.0000003 0.0000002 3795 tags=36%, list=17%, signal=30%
DOID:16 integumentary system disease 344 -0.5237988 -1.799146 0.0000000 0.0000003 0.0000002 3795 tags=35%, list=17%, signal=29%
DOID:7148 rheumatoid arthritis 491 -0.4850823 -1.698319 0.0000000 0.0000003 0.0000002 4515 tags=36%, list=21%, signal=29%
DOID:2723 dermatitis 154 -0.5981187 -1.925163 0.0000000 0.0000031 0.0000023 2996 tags=39%, list=14%, signal=34%
DOID:850 lung disease 448 -0.4567010 -1.596029 0.0000015 0.0001963 0.0001434 3851 tags=32%, list=18%, signal=27%
DOID:0050161 lower respiratory tract disease 457 -0.4539550 -1.589149 0.0000023 0.0002485 0.0001815 3851 tags=32%, list=18%, signal=27%
DOID:3310 atopic dermatitis 123 -0.5959388 -1.859411 0.0000026 0.0002485 0.0001815 2996 tags=39%, list=14%, signal=34%
DOID:0050737 autosomal recessive disease 304 -0.4853740 -1.656777 0.0000032 0.0002641 0.0001929 2996 tags=24%, list=14%, signal=21%
DOID:104 bacterial infectious disease 232 -0.5157119 -1.728091 0.0000048 0.0003537 0.0002583 3226 tags=33%, list=15%, signal=28%
DOID:74 hematopoietic system disease 430 -0.4442370 -1.547017 0.0000086 0.0005699 0.0004163 3706 tags=29%, list=17%, signal=24%
DOID:2349 arteriosclerosis 321 -0.4602345 -1.573708 0.0000153 0.0009202 0.0006721 4291 tags=36%, list=20%, signal=30%
DOID:0050338 primary bacterial infectious disease 203 -0.5092871 -1.682387 0.0000199 0.0010927 0.0007982 3226 tags=33%, list=15%, signal=28%
DOID:170 endocrine gland cancer 476 -0.4300668 -1.505744 0.0000231 0.0011748 0.0008582 3931 tags=28%, list=18%, signal=23%
DOID:1936 atherosclerosis 310 -0.4567575 -1.561612 0.0000561 0.0026424 0.0019302 4251 tags=36%, list=19%, signal=30%
DOID:0070004 myeloma 296 -0.4613705 -1.572658 0.0000621 0.0027322 0.0019958 4395 tags=36%, list=20%, signal=30%
DOID:3213 demyelinating disease 159 -0.5143553 -1.658572 0.0000978 0.0040337 0.0029465 4866 tags=46%, list=22%, signal=36%
DOID:0060005 autoimmune disease of endocrine system 81 -0.5958219 -1.753721 0.0001071 0.0041588 0.0030378 3163 tags=41%, list=14%, signal=35%
DOID:2348 arteriosclerotic cardiovascular disease 311 -0.4559921 -1.559441 0.0001270 0.0043696 0.0031918 4251 tags=36%, list=19%, signal=29%
DOID:10241 thalassemia 42 -0.6927320 -1.876801 0.0001284 0.0043696 0.0031918 1180 tags=24%, list=5%, signal=23%
DOID:526 Human immunodeficiency virus infectious disease 156 -0.5141764 -1.653475 0.0001385 0.0043696 0.0031918 3795 tags=33%, list=17%, signal=28%
DOID:4960 bone marrow cancer 301 -0.4578960 -1.562517 0.0001390 0.0043696 0.0031918 4395 tags=36%, list=20%, signal=29%
DOID:28 endocrine system disease 342 -0.4378120 -1.503976 0.0001514 0.0044404 0.0032436 3163 tags=27%, list=14%, signal=23%
DOID:1883 hepatitis C 211 -0.4812333 -1.601759 0.0001547 0.0044404 0.0032436 3154 tags=27%, list=14%, signal=24%
DOID:50 thyroid gland disease 144 -0.5144514 -1.636812 0.0001940 0.0053347 0.0038968 3714 tags=36%, list=17%, signal=30%
DOID:1398 parasitic infectious disease 130 -0.5231347 -1.640957 0.0002270 0.0059264 0.0043290 4278 tags=43%, list=20%, signal=35%
DOID:9538 multiple myeloma 241 -0.4653044 -1.563090 0.0002423 0.0059264 0.0043290 4448 tags=36%, list=20%, signal=29%
DOID:403 mouth disease 164 -0.5004962 -1.621306 0.0002451 0.0059264 0.0043290 3262 tags=35%, list=15%, signal=30%
DOID:2320 obstructive lung disease 279 -0.4562386 -1.549021 0.0002514 0.0059264 0.0043290 3360 tags=30%, list=15%, signal=26%
DOID:9778 irritable bowel syndrome 68 -0.5999453 -1.740745 0.0002788 0.0063451 0.0046349 3703 tags=41%, list=17%, signal=34%
DOID:7998 hyperthyroidism 89 -0.5623924 -1.682362 0.0002896 0.0063703 0.0046533 3163 tags=37%, list=14%, signal=32%

Top 30 most significant Disease Ontology - NCG - Network of Cancer Gene

Description setSize enrichmentScore NES pvalue p.adjust qvalues rank leading_edge
neuroblastoma neuroblastoma 55 -0.5503364 -1.5583495 0.0103474 0.5294026 0.5234923 4272 tags=35%, list=20%, signal=28%
small_cell_lung_cancer small_cell_lung_cancer 48 -0.5457921 -1.5029106 0.0177137 0.5294026 0.5234923 2103 tags=35%, list=10%, signal=32%
squamous_head_and_neck_cancer squamous_head_and_neck_cancer 106 -0.4469183 -1.3806279 0.0240638 0.5294026 0.5234923 4303 tags=35%, list=20%, signal=28%
cutaneous_DLBCL cutaneous_DLBCL 21 -0.6323672 -1.5012498 0.0460751 0.7602389 0.7517514 2810 tags=29%, list=13%, signal=25%
cutaneous_T_cell_lymphoma cutaneous_T_cell_lymphoma 25 -0.5639416 -1.3876083 0.0861789 1.0000000 0.9888357 5318 tags=60%, list=24%, signal=45%
acute_promyelocytic_leukemia acute_promyelocytic_leukemia 29 -0.5463150 -1.3857295 0.0956938 1.0000000 0.9888357 5121 tags=34%, list=23%, signal=26%
Burkitt's_lymphoma Burkitt's_lymphoma 21 -0.5582202 -1.3252237 0.1331058 1.0000000 0.9888357 1992 tags=33%, list=9%, signal=30%
desmoplastic_melanoma desmoplastic_melanoma 24 -0.5353084 -1.3073673 0.1414309 1.0000000 0.9888357 708 tags=21%, list=3%, signal=20%
juvenile_myelomonocytic_leukemia juvenile_myelomonocytic_leukemia 16 -0.5876466 -1.3120453 0.1443478 1.0000000 0.9888357 4865 tags=31%, list=22%, signal=24%
esophageal_squamous_carcinoma esophageal_squamous_carcinoma 42 -0.4575009 -1.2248149 0.1886792 1.0000000 0.9888357 4474 tags=43%, list=21%, signal=34%
glioblastoma glioblastoma 107 0.3170657 1.1245008 0.2022059 1.0000000 0.9888357 753 tags=8%, list=3%, signal=8%
T-cell_leukemia/lymphoma T-cell_leukemia/lymphoma 49 -0.4279030 -1.1857387 0.2233883 1.0000000 0.9888357 5182 tags=35%, list=24%, signal=27%
chronic_lymphocytic_leukemia chronic_lymphocytic_leukemia 108 -0.3629755 -1.1226889 0.2735978 1.0000000 0.9888357 4251 tags=28%, list=19%, signal=22%
pancreatic_ductal_adenocarcinoma pancreatic_ductal_adenocarcinoma 150 -0.3433403 -1.0958340 0.2752294 1.0000000 0.9888357 3779 tags=23%, list=17%, signal=19%
esophageal_adenocarcinoma esophageal_adenocarcinoma 42 -0.4214600 -1.1283267 0.3018868 1.0000000 0.9888357 2578 tags=21%, list=12%, signal=19%
pan-cancer_paediatric pan-cancer_paediatric 174 -0.3345652 -1.0847952 0.3029151 1.0000000 0.9888357 4576 tags=20%, list=21%, signal=16%
soft_tissue_sarcoma soft_tissue_sarcoma 25 -0.4609154 -1.1341069 0.3138211 1.0000000 0.9888357 4251 tags=40%, list=19%, signal=32%
skin_basal_cell_carcinoma skin_basal_cell_carcinoma 25 -0.4291984 -1.0560654 0.3886179 1.0000000 0.9888357 4344 tags=32%, list=20%, signal=26%
ovarian_cancer ovarian_cancer 16 -0.4765402 -1.0639767 0.3930435 1.0000000 0.9888357 5458 tags=38%, list=25%, signal=28%
natural_killer/T_cell_lymphoma natural_killer/T_cell_lymphoma 25 -0.4248910 -1.0454669 0.3983740 1.0000000 0.9888357 6191 tags=40%, list=28%, signal=29%
melanoma melanoma 127 -0.3198396 -1.0071912 0.4401596 1.0000000 0.9888357 4831 tags=25%, list=22%, signal=20%
paediatric_low_grade_glioma paediatric_low_grade_glioma 33 -0.3943560 -1.0188613 0.4414557 1.0000000 0.9888357 4758 tags=33%, list=22%, signal=26%
non-small_cell_lung_cancer non-small_cell_lung_cancer 25 -0.4103357 -1.0096527 0.4455285 1.0000000 0.9888357 5966 tags=48%, list=27%, signal=35%
lung_cancer_(all_histologies) lung_cancer_(all_histologies) 90 -0.3341799 -1.0076238 0.4498607 1.0000000 0.9888357 5966 tags=29%, list=27%, signal=21%
triple_negative_breast_cancer triple_negative_breast_cancer 75 -0.3378662 -0.9940391 0.4837341 1.0000000 0.9888357 4805 tags=23%, list=22%, signal=18%
colorectal_adenocarcinoma colorectal_adenocarcinoma 150 -0.2961113 -0.9450940 0.5766710 1.0000000 0.9888357 3619 tags=19%, list=17%, signal=16%
pan-liver pan-liver 28 -0.3597050 -0.9074588 0.5961538 1.0000000 0.9888357 1495 tags=36%, list=7%, signal=33%
esophageal_(squamous_and_adenocarcinoma) esophageal_(squamous_and_adenocarcinoma) 17 -0.4035685 -0.9085658 0.6052632 1.0000000 0.9888357 5966 tags=35%, list=27%, signal=26%
acute_lymphoblastic_leukemia acute_lymphoblastic_leukemia 49 -0.3245775 -0.8994191 0.6251874 1.0000000 0.9888357 5032 tags=31%, list=23%, signal=24%
chronic_myeloid_leukemia chronic_myeloid_leukemia 28 -0.3431107 -0.8655949 0.6538462 1.0000000 0.9888357 2737 tags=14%, list=13%, signal=13%

Top 30 most significant Disease Ontology - DGN - Disease Gene Network

Description setSize enrichmentScore NES pvalue p.adjust qvalues rank leading_edge
C4551906 Ciliary Dyskinesia, Primary, 1, With Or Without Situs Inversus 40 0.7877550 2.358369 0.0e+00 0.0000119 0.0000103 4344 tags=92%, list=20%, signal=74%
C0271994 Hereditary persistence of fetal hemoglobin thalassemia 28 -0.8729034 -2.207257 0.0e+00 0.0000119 0.0000103 46 tags=18%, list=0%, signal=18%
C0021368 Inflammation 422 -0.4894970 -1.704487 0.0e+00 0.0000119 0.0000103 4251 tags=38%, list=19%, signal=31%
C0409974 Lupus Erythematosus 476 -0.4784378 -1.675145 0.0e+00 0.0000197 0.0000171 4260 tags=33%, list=20%, signal=27%
C1855672 Immotile cilia 37 0.7911813 2.331074 0.0e+00 0.0000197 0.0000171 4344 tags=95%, list=20%, signal=76%
C4703436 Impaired nasal mucociliary clearance 37 0.7911813 2.331074 0.0e+00 0.0000197 0.0000171 4344 tags=95%, list=20%, signal=76%
C0024138 Lupus Erythematosus, Discoid 469 -0.4776091 -1.671969 0.0e+00 0.0000197 0.0000171 4260 tags=33%, list=20%, signal=27%
C0024131 Lupus Vulgaris 445 -0.4789220 -1.672634 0.0e+00 0.0000261 0.0000226 4175 tags=32%, list=19%, signal=27%
C0037284 Skin lesion 488 -0.4691077 -1.645420 0.0e+00 0.0000261 0.0000226 4335 tags=34%, list=20%, signal=28%
C0022521 Kartagener Syndrome 62 0.6985629 2.277271 0.0e+00 0.0000261 0.0000226 4469 tags=79%, list=20%, signal=63%
C0031090 Periodontal Diseases 282 -0.5180367 -1.757942 0.0e+00 0.0000261 0.0000226 3851 tags=39%, list=18%, signal=32%
C0026896 Myasthenia Gravis 289 -0.5241955 -1.781566 0.0e+00 0.0000261 0.0000226 3844 tags=38%, list=18%, signal=32%
C0398650 Immune thrombocytopenic purpura 279 -0.5182311 -1.759283 1.0e-07 0.0000261 0.0000226 3550 tags=36%, list=16%, signal=31%
C4317124 Polynesian Bronchiectasis 33 0.7917827 2.252494 1.0e-07 0.0000297 0.0000257 4300 tags=94%, list=20%, signal=76%
C0002895 Anemia, Sickle Cell 374 -0.4876633 -1.689971 1.0e-07 0.0000608 0.0000527 2996 tags=23%, list=14%, signal=20%
C0018520 Halitosis 44 0.7347740 2.268959 2.0e-07 0.0000717 0.0000621 4344 tags=86%, list=20%, signal=69%
C0003862 Arthralgia 233 -0.5308531 -1.779000 2.0e-07 0.0000840 0.0000728 4169 tags=35%, list=19%, signal=29%
C0037299 Skin Ulcer 141 -0.5907092 -1.894404 4.0e-07 0.0001330 0.0001152 4625 tags=38%, list=21%, signal=30%
C0867389 Chronic graft-versus-host disease 205 -0.5401337 -1.787557 4.0e-07 0.0001488 0.0001289 3154 tags=32%, list=14%, signal=28%
C0008780 Ciliary Motility Disorders 52 0.6972746 2.226624 5.0e-07 0.0001566 0.0001357 4344 tags=75%, list=20%, signal=60%
C0036202 Sarcoidosis 350 -0.4842089 -1.677871 5.0e-07 0.0001566 0.0001357 3844 tags=31%, list=18%, signal=26%
C0011603 Dermatitis 439 -0.4648286 -1.621206 6.0e-07 0.0001794 0.0001554 4251 tags=33%, list=19%, signal=27%
C0031106 Aggressive Periodontitis 159 -0.5693921 -1.849226 6.0e-07 0.0001794 0.0001554 3208 tags=38%, list=15%, signal=33%
C0014060 Encephalitis, St. Louis 234 -0.5262600 -1.762663 9.0e-07 0.0002435 0.0002109 4291 tags=37%, list=20%, signal=30%
C0024314 Lymphoproliferative Disorders 258 -0.5118530 -1.720976 1.0e-06 0.0002593 0.0002246 3762 tags=33%, list=17%, signal=28%
C0023440 Acute Erythroblastic Leukemia 264 -0.4965192 -1.671357 1.9e-06 0.0004753 0.0004118 4391 tags=26%, list=20%, signal=21%
C1527336 Sjogren’s Syndrome 414 -0.4546769 -1.585085 2.4e-06 0.0005934 0.0005140 3238 tags=26%, list=15%, signal=22%
C0022568 Keratitis 143 -0.5763912 -1.855153 2.7e-06 0.0006116 0.0005298 4105 tags=37%, list=19%, signal=30%
C0011311 Dengue Fever 315 -0.4879311 -1.670805 2.7e-06 0.0006116 0.0005298 4413 tags=30%, list=20%, signal=24%
C0042109 Urticaria 154 -0.5681084 -1.839187 2.8e-06 0.0006116 0.0005298 4225 tags=42%, list=19%, signal=34%

Table of DEGs

id hgnc baseMean log2FoldChange lfcSE stat pvalue padj
ENSG00000004799 PDK4 1774.517985 1.8073989 0.3037663 5.949964 0.0000000 0.0000154
ENSG00000070540 WIPI1 5069.961230 0.6430208 0.1568302 4.100108 0.0000413 0.0400580
ENSG00000071242 RPS6KA2 10519.642406 0.6464711 0.1690594 3.823928 0.0001313 0.0877147
ENSG00000078898 BPIFB2 1321.895646 -2.6947052 0.7193037 -3.746269 0.0001795 0.0980175
ENSG00000085265 FCN1 111.670183 -2.0733475 0.5542423 -3.740868 0.0001834 0.0980175
ENSG00000087495 PHACTR3 385.304675 2.7849520 0.4549762 6.121093 0.0000000 0.0000071
ENSG00000096060 FKBP5 9841.538419 2.7571923 0.3597548 7.664087 0.0000000 0.0000000
ENSG00000101916 TLR8 100.381433 -1.7918440 0.4196173 -4.270187 0.0000195 0.0250887
ENSG00000103942 HOMER2 5443.869611 0.6212210 0.1474074 4.214312 0.0000251 0.0303062
ENSG00000109906 ZBTB16 19666.248173 2.9924653 0.5195812 5.759380 0.0000000 0.0000323
ENSG00000111666 CHPT1 5157.328919 0.7817596 0.2016591 3.876640 0.0001059 0.0760657
ENSG00000117152 RGS4 285.956946 -1.8641446 0.5003152 -3.725940 0.0001946 0.0993828
ENSG00000117479 SLC19A2 2324.977435 0.7186033 0.1898646 3.784819 0.0001538 0.0937895
ENSG00000119138 KLF9 2951.813358 1.0598054 0.2728519 3.884178 0.0001027 0.0760657
ENSG00000125538 IL1B 46.029969 -1.5333992 0.4060738 -3.776159 0.0001593 0.0937895
ENSG00000151012 SLC7A11 3805.816974 -3.0110722 0.6992094 -4.306395 0.0000166 0.0238357
ENSG00000154277 UCHL1 422.690325 -2.5745162 0.6577718 -3.913996 0.0000908 0.0719456
ENSG00000157514 TSC22D3 4388.619107 1.2398592 0.2022905 6.129104 0.0000000 0.0000071
ENSG00000163053 SLC16A14 1065.539780 1.1320323 0.2997478 3.776616 0.0001590 0.0937895
ENSG00000163563 MNDA 368.878123 -1.8258115 0.4526803 -4.033336 0.0000550 0.0505540
ENSG00000163884 KLF15 621.988003 1.4280049 0.3300281 4.326919 0.0000151 0.0231683
ENSG00000170820 FSHR 49.752910 -2.5502589 0.6467712 -3.943062 0.0000804 0.0684790
ENSG00000171658 NMRAL2P 512.290404 -2.9991002 0.6585254 -4.554267 0.0000053 0.0120819
ENSG00000173391 OLR1 98.232524 -2.0428788 0.4937278 -4.137662 0.0000351 0.0366540
ENSG00000186407 CD300E 23.227454 -2.4125659 0.5651571 -4.268841 0.0000196 0.0250887
ENSG00000188269 OR7A5 68.793359 2.3794778 0.5061446 4.701182 0.0000026 0.0072383
ENSG00000188536 HBA2 637.909397 -3.0218702 0.8015523 -3.770022 0.0001632 0.0937895
ENSG00000196208 GREB1 211.601669 1.7238554 0.4493969 3.835931 0.0001251 0.0871193
ENSG00000197629 MPEG1 556.151502 -1.3979913 0.3560533 -3.926354 0.0000862 0.0707904
ENSG00000211951 IGHV2-26 27.070247 -3.3078799 0.7441421 -4.445226 0.0000088 0.0168158
ENSG00000227610 FRMPD3-AS1 47.872542 2.1280625 0.5484509 3.880133 0.0001044 0.0760657
ENSG00000230978 LINC00160 8.311309 2.1746036 0.5723650 3.799330 0.0001451 0.0926264
ENSG00000235303 14.970215 -1.1506977 0.3062695 -3.757141 0.0001719 0.0963410
ENSG00000248165 685.740404 -2.8353226 0.6055194 -4.682464 0.0000028 0.0072383
ENSG00000249717 PARM1-AS1 66.066138 -2.6893581 0.6147719 -4.374563 0.0000122 0.0199749
ENSG00000250994 73.980616 0.9156424 0.2453721 3.731648 0.0001902 0.0993655
ENSG00000251003 ZFPM2-AS1 589.691311 -2.1213612 0.5177677 -4.097129 0.0000418 0.0400580
ENSG00000258038 LINC02327 28.764284 -3.3843759 0.8860163 -3.819767 0.0001336 0.0877147
ENSG00000259479 SORD2P 1389.845136 2.4724575 0.6228792 3.969401 0.0000721 0.0636925
ENSG00000260186 LINC02137 165.324032 1.6962819 0.4036752 4.202096 0.0000264 0.0303898
ENSG00000262039 39.871203 1.3363845 0.3048105 4.384313 0.0000116 0.0199749
ENSG00000267594 CYP4F24P 72.684971 -2.4885693 0.5990410 -4.154255 0.0000326 0.0357165
ENSG00000267653 19.727419 3.4695816 0.7069850 4.907574 0.0000009 0.0030275
ENSG00000259176 NA 23.971388 2.5873311 0.5722578 4.521269 0.0000061 0.0128433

Number of DEGs: 44

COL + MMP + TIMP

id hgnc baseMean log2FoldChange lfcSE stat pvalue padj
ENSG00000008516 MMP25 47.814331 -0.7299385 0.4159684 -1.7547932 0.0792947 0.9997399
ENSG00000035862 TIMP2 2017.994671 -0.4488761 0.4639810 -0.9674449 0.3333217 0.9997399
ENSG00000049089 COL9A2 386.467175 0.3580127 0.3394490 1.0546877 0.2915682 0.9997399
ENSG00000050767 COL23A1 1797.394008 -0.5426821 0.4435741 -1.2234307 0.2211671 0.9997399
ENSG00000060718 COL11A1 29.954148 -0.8439206 0.5376557 -1.5696302 0.1165012 0.9997399
ENSG00000065618 COL17A1 2627.563451 -0.1407201 0.4879729 -0.2883770 0.7730582 0.9997399
ENSG00000080573 COL5A3 333.831459 -0.2943238 0.5489190 -0.5361880 0.5918286 0.9997399
ENSG00000081052 COL4A4 415.076341 0.1635917 0.3886385 0.4209354 0.6738022 0.9997399
ENSG00000082293 COL19A1 1865.136149 -0.0534734 0.5306025 -0.1007786 0.9197262 0.9997399
ENSG00000084636 COL16A1 2277.626966 -0.2495544 0.3468906 -0.7194037 0.4718922 0.9997399
ENSG00000087245 MMP2 1910.858902 -0.4224581 0.5245800 -0.8053264 0.4206314 0.9997399
ENSG00000092758 COL9A3 64.032653 -0.6456897 0.3770181 -1.7126228 0.0867820 0.9997399
ENSG00000099953 MMP11 40.287877 -0.4082052 0.3112927 -1.3113230 0.1897487 0.9997399
ENSG00000100234 TIMP3 13237.910809 0.0601797 0.4590161 0.1311058 0.8956916 0.9997399
ENSG00000100985 MMP9 13.945728 0.2194338 0.6796597 0.3228583 0.7468025 0.9997399
ENSG00000101203 COL20A1 2.608173 -0.0299840 0.7574789 -0.0395839 0.9684248 NA
ENSG00000102265 TIMP1 1329.899651 -0.2097742 0.2393428 -0.8764594 0.3807804 0.9997399
ENSG00000102996 MMP15 259.630827 -0.1744123 0.2637980 -0.6611586 0.5085106 0.9997399
ENSG00000108821 COL1A1 1250.766296 -0.8890248 0.4970015 -1.7887768 0.0736508 0.9997399
ENSG00000111799 COL12A1 4539.497308 -0.2735144 0.4351595 -0.6285383 0.5296514 0.9997399
ENSG00000112280 COL9A1 23.330406 -0.1182665 0.4332886 -0.2729509 0.7848909 0.9997399
ENSG00000114270 COL7A1 4754.168226 -0.3950842 0.4129055 -0.9568394 0.3386483 0.9997399
ENSG00000118113 MMP8 1.302535 -2.6725619 1.0098230 -2.6465646 0.0081314 NA
ENSG00000123342 MMP19 126.856936 -0.0005803 0.3901390 -0.0014875 0.9988132 0.9999329
ENSG00000123500 COL10A1 42.034741 -0.5144431 0.5141438 -1.0005821 0.3170289 0.9997399
ENSG00000125966 MMP24 54.115356 -0.0458827 0.3330566 -0.1377624 0.8904282 0.9997399
ENSG00000130635 COL5A1 2973.745763 -0.9567757 0.4878958 -1.9610247 0.0498761 0.9625525
ENSG00000134871 COL4A2 7220.286767 -0.3562504 0.5629478 -0.6328302 0.5268445 0.9997399
ENSG00000137673 MMP7 87.850186 -0.3493016 0.5000304 -0.6985608 0.4848266 0.9997399
ENSG00000137674 MMP20 2.280935 -0.9137534 0.5505163 -1.6598117 0.0969523 NA
ENSG00000137675 MMP27 36.109287 -0.6663520 0.5771123 -1.1546315 0.2482414 0.9997399
ENSG00000137745 MMP13 164.396539 -0.9656219 0.4466950 -2.1617032 0.0306411 0.8182963
ENSG00000142156 COL6A1 2292.773568 -0.1282887 0.5398690 -0.2376293 0.8121686 0.9997399
ENSG00000142173 COL6A2 3760.422733 -0.2263442 0.5781825 -0.3914753 0.6954459 0.9997399
ENSG00000144810 COL8A1 3009.510362 0.1409280 0.4174245 0.3376132 0.7356547 0.9997399
ENSG00000149968 MMP3 7.315606 0.2899462 0.5696511 0.5089892 0.6107598 NA
ENSG00000154485 MMP21 22.801905 0.1610517 0.2395699 0.6722533 0.5014225 0.9997399
ENSG00000156103 MMP16 1643.589280 0.0596325 0.4575780 0.1303220 0.8963117 0.9997399
ENSG00000157150 TIMP4 296.721191 0.0129175 0.5545784 0.0232924 0.9814170 0.9997399
ENSG00000157227 MMP14 1919.957690 -0.3502053 0.1793489 -1.9526481 0.0508613 0.9638958
ENSG00000160963 COL26A1 70.986141 -0.8950093 0.3341566 -2.6784129 0.0073972 0.4899418
ENSG00000163359 COL6A3 8648.461070 -0.0885335 0.4698139 -0.1884437 0.8505289 0.9997399
ENSG00000164692 COL1A2 5960.134146 -0.7604720 0.5302002 -1.4343111 0.1514835 0.9997399
ENSG00000166670 MMP10 1432.539174 -0.2000672 0.6276028 -0.3187800 0.7498934 0.9997399
ENSG00000168542 COL3A1 8154.537217 -0.6517421 0.5249876 -1.2414429 0.2144422 0.9997399
ENSG00000169031 COL4A3 263.147839 0.1541405 0.4007592 0.3846212 0.7005181 0.9997399
ENSG00000169436 COL22A1 144.692102 -0.5120219 0.3960596 -1.2927901 0.1960837 0.9997399
ENSG00000171502 COL24A1 1347.161170 -0.0024750 0.2059044 -0.0120201 0.9904096 0.9997399
ENSG00000171812 COL8A2 167.235545 -0.6708193 0.4564343 -1.4696952 0.1416443 0.9997399
ENSG00000172752 COL6A5 424.199656 -0.1578098 0.6223145 -0.2535853 0.7998159 0.9997399
ENSG00000182871 COL18A1 2389.763209 -0.7129194 0.4466833 -1.5960287 0.1104824 0.9997399
ENSG00000187498 COL4A1 5728.448623 -0.4255553 0.5366124 -0.7930404 0.4277543 0.9997399
ENSG00000187955 COL14A1 4041.229187 -0.4447637 0.3976846 -1.1183830 0.2634034 0.9997399
ENSG00000188153 COL4A5 39671.258609 -0.0626492 0.2442341 -0.2565131 0.7975547 0.9997399
ENSG00000188517 COL25A1 1879.068967 -0.2395182 0.2824181 -0.8480979 0.3963835 0.9997399
ENSG00000196739 COL27A1 2160.128640 -0.4148415 0.3364760 -1.2329009 0.2176127 0.9997399
ENSG00000197467 COL13A1 1933.455231 -0.2268017 0.5820697 -0.3896470 0.6967976 0.9997399
ENSG00000197565 COL4A6 12907.999858 -0.1371358 0.3582945 -0.3827460 0.7019081 0.9997399
ENSG00000198598 MMP17 106.982523 -0.6663581 0.4831654 -1.3791512 0.1678482 0.9997399
ENSG00000204248 COL11A2 55.943700 -0.1796276 0.3481300 -0.5159784 0.6058695 0.9997399
ENSG00000204262 COL5A2 4827.335133 0.0950911 0.2530289 0.3758113 0.7070572 0.9997399
ENSG00000204291 COL15A1 7301.702970 -0.5394266 0.5283291 -1.0210048 0.3072522 0.9997399
ENSG00000206384 COL6A6 671.641676 -0.6482451 0.6373286 -1.0171285 0.3090923 0.9997399
ENSG00000215018 COL28A1 9611.717135 0.3921716 0.4097600 0.9570765 0.3385286 0.9997399